% Encoding: windows-1252

@MANUAL{RCoreTeam2015,
  title = {\proglang{R}: A Language and Environment for Statistical Computing},
  author = {{\proglang{R} Core Team}},
  organization = {\proglang{R} Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2018},
  owner = {Satu Helske},
  timestamp = {2015.12.16},
  url = {http://www.R-project.org/}
}

@ARTICLE{Aisenbrey2010,
  author = {Aisenbrey, S. and Fasang, A.E.},
  title = {New Life for Old Ideas: The ``Second Wave'' of Sequence Analysis
	-- Bringing the ``Course'' Back Into the Life Course},
  journal = {Sociological Methods \& Research},
  year = {2010},
  volume = {38},
  pages = {420--462},
  number = {3},
  doi = {10.1177/0049124109357532},
}

@MANUAL{Bartolucci2015,
  title = {\pkg{LMest}: Latent Markov Models with and without Covariates},
  author = {Bartolucci, Francesco and Pandolfi, Silvia},
  year = {2015},
  note = {\proglang{R}~Package Version~2.1},
  owner = {Satu Helske},
  timestamp = {2015.12.16},
  url = {http://CRAN.R-project.org/package=LMest}
}

@ARTICLE{Baum1966,
  author = {Baum, Leonard E and Petrie, Ted},
  title = {Statistical Inference for Probabilistic Functions of Finite State
	Markov Chains},
  journal = {The Annals of Mathematical Statistics},
  year = {1966},
  volume = {67},
  pages = {1554--1563},
  number = {6},
  doi = {10.1214/aoms/1177699147},
  owner = {Satu Helske},
  publisher = {JSTOR},
  timestamp = {2015.04.22}
}

@ARTICLE{Collins1992,
  author = {Collins, Linda M and Wugalter, Stuart E},
  title = {Latent Class Models for Stage-Sequential Dynamic Latent Variables},
  journal = {Multivariate Behavioral Research},
  year = {1992},
  volume = {27},
  pages = {131--157},
  number = {1},
  doi = {10.1207/s15327906mbr2701_8},
  owner = {Satu Helske},
  publisher = {Taylor \& Francis},
  timestamp = {2015.11.25}
}

@ARTICLE{Csardi2006,
  author = {Csardi, Gabor and Nepusz, Tamas},
  title = {The \pkg{igraph} Software Package for Complex Network Research},
  journal = {InterJournal Complex Systems},
  year = {2006},
  volume = {1695},
  owner = {Satu Helske},
  timestamp = {2015.06.09},
  url = {http://igraph.org}
}

@ARTICLE{Dagum1998,
  author = {Dagum, Leonardo and Enon, Rameshm},
  title = {OpenMP: An Industry Standard API for Shared-Memory Programming},
  journal = {Computational Science \& Engineering, IEEE},
  year = {1998},
  volume = {5},
  pages = {46-55},
  number = {1},
  owner = {Satu Helske},
  publisher = {IEEE},
  timestamp = {2016.02.10}
}

@BOOK{Durbin1998,
  title = {Biological Sequence Analysis: Probabilistic Models of Proteins and
	Nucleic Acids},
  publisher = {Cambridge University Press},
  year = {1998},
  author = {Durbin, R. and Eddy, S.R. and Krogh, A. and Mitchison, G.},
  address = {Cambridge, UK},
  owner = {Satu Helske},
  timestamp = {2009.12.08}
}

@BOOK{Eddelbuettel2013,
  title = {Seamless \proglang{R} and \proglang{C++} Integration with \pkg{Rcpp}},
  publisher = {Springer-Verlag},
  year = {2013},
  author = {Dirk Eddelbuettel},
  address = {New York},
  note = {ISBN 978-1-4614-6867-7},
  owner = {Satu Helske},
  timestamp = {2015.12.07}
}

@ARTICLE{Eddelbuettel2011,
  author = {Dirk Eddelbuettel and Romain Fran\c{c}ois},
  title = {\pkg{Rcpp}: Seamless \proglang{R} and \proglang{C++} Integration},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  pages = {1--18},
  number = {8},
  doi = {10.18637/jss.v040.i08},
  owner = {Satu Helske},
  timestamp = {2015.12.07}
}

@ARTICLE{Eddelbuettel2014,
  author = {Dirk Eddelbuettel and Conrad Sanderson},
  title = {\proglang{RcppArmadillo}: Accelerating \proglang{R} with High-Performance
	\proglang{C++} Linear Algebra},
  journal = {Computational Statistics and Data Analysis},
  year = {2014},
  volume = {71},
  pages = {1054--1063},
  month = {March},
  doi = {10.1016/j.csda.2013.02.005},
  owner = {Satu Helske},
  timestamp = {2015.12.07}
}

@ARTICLE{Elzinga2014,
  author = {Elzinga, Cees H and Studer, Matthias},
  title = {Spell Sequences, State Proximities, and Distance Metrics},
  journal = {Sociological Methods \& Research},
  year = {2014},
  pages = {3--47},
  doi = {10.1177/0049124114540707},
  owner = {Satu Helske},
  publisher = {SAGE Publications},
  timestamp = {2015.05.15}
}

@ARTICLE{Gabadinho2011,
  author = {Gabadinho, Alexis and Ritschard, Gilbert and M{\"u}ller, Nicolas
	S. and Studer, Matthias},
  title = {Analyzing and Visualizing State Sequences in \proglang{R} with \pkg{TraMineR}},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {40},
  pages = {1--37},
  number = {4},
  doi = {10.18637/jss.v040.i04},
  owner = {Satu Helske},
  publisher = {American Statistical Association},
  timestamp = {2011.06.22}
}

@ARTICLE{Gauthier2010,
  author = {Gauthier, Jacques-Antoine and Widmer, Eric D. and Bucher, Philipp
	and Notredame, C\'{e}dric},
  title = {Multichannel Sequence Analysis Applied to Social Science Data},
  journal = {Sociological Methodology},
  year = {2010},
  volume = {40},
  pages = {1--38},
  number = {1},
  doi = {10.1111/j.1467-9531.2010.01227.x},
  owner = {Satu Helske},
  publisher = {Wiley Online Library},
  timestamp = {2011.06.21}
}

@ARTICLE{Gauthier2009,
  author = {Gauthier, Jacques-Antoine and Widmer, Eric D and Bucher, Philipp
	and Notredame, C{\'e}dric},
  title = {How Much Does It Cost? Optimization of Costs in Sequence Analysis
	of Social Science Data},
  journal = {Sociological Methods \& Research},
  year = {2009},
  volume = {38},
  pages = {197--231},
  number = {1},
  doi = {10.1177/0049124109342065},
  owner = {Satu Helske},
  publisher = {Sage Publications},
  timestamp = {2014.06.12}
}

@ARTICLE{Halpin2010,
  author = {Brendan Halpin},
  title = {Optimal Matching Analysis and Life-Course Data: The Importance of
	Duration},
  journal = {Sociological Methods \& Research},
  year = {2010},
  volume = {38},
  pages = {365--388},
  number = {3},
  doi = {10.1177/0049124110363590},
  owner = {Satu Helske},
  timestamp = {2010.05.24}
}

@MANUAL{Himmelmann2010,
  title = {\pkg{HMM} -- Hidden Markov Models},
  author = {Himmelmann, Lin},
  year = {2010},
  note = {\proglang{R}~Package Version~1.0},
  owner = {Satu Helske},
  timestamp = {2015.04.21},
  url = {http://CRAN.R-project.org/package=HMM}
}

@ARTICLE{Hollister2009,
  author = {Hollister, Matissa},
  title = {Is Optimal Matching Suboptimal?},
  journal = {Sociological Methods \& Research},
  year = {2009},
  volume = {38},
  pages = {235--264},
  number = {2},
  doi = {10.1177/0049124109346164},
  owner = {Satu Helske},
  publisher = {Sage Publications},
  timestamp = {2011.06.20}
}

@ARTICLE{Jackson2011,
  author = {Christopher H. Jackson},
  title = {Multi-State Models for Panel Data: The \pkg{msm} Package for \proglang{R}},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {38},
  pages = {1--29},
  number = {8},
  doi = {10.18637/jss.v038.i08},
  owner = {Satu Helske},
  timestamp = {2015.12.07}
}

@MANUAL{nlopt,
  title = {The NLopt Nonlinear Optimization Package},
  author = {Steven G Johnson},
  year = {2014},
  owner = {Satu Helske},
  timestamp = {2015.08.24},
  url = {http://ab-initio.mit.edu/nlopt}
}

@ARTICLE{Kucherenko2005,
  author = {Kucherenko, Sergei and Sytsko, Yury},
  title = {Application of Deterministic Low-Discrepancy Sequences in Global
	Optimization},
  journal = {Computational Optimization and Applications},
  year = {2005},
  volume = {30},
  pages = {297--318},
  number = {3},
  doi = {10.1007/s10589-005-4615-1},
  owner = {Satu Helske},
  publisher = {Springer},
  timestamp = {2015.08.26}
}

@ARTICLE{Lesnard2010,
  author = {Lesnard, Laurent},
  title = {Setting Cost in Optimal Matching to Uncover Contemporaneous Socio-Temporal
	Patterns},
  journal = {Sociological Methods \& Research},
  year = {2010},
  volume = {38},
  pages = {389--419},
  number = {3},
  abstract = {This article addresses the question of the effects of cost setting
	on the kind of temporal patterns optimal matching (OM) can uncover
	when applied to social science data. It is argued that the balance
	between indel (insertion and deletion) and substitution costs determines
	what kind of socio-temporal pattern can be brought to light. Insertion
	and deletion operations favor identically coded states irrespective
	of their locations whereas substitutions focus on contemporaneous
	similarities. The lower the ratio of substitution to indel costs,
	the closer OM is to the Hamming distance where only substitutions
	are used. The higher this ratio, the closer OM is to the Levenshtein
	II distance, which amounts to finding the longest common subsequence.
	When the timing of sequences is crucial, substitutions should be
	favored over indels and their costs should be carefully fixed. Ideally,
	substitution costs should vary with time to better take into account
	the timing of the sequences studied. As indels warp time, hence the
	timing of sequences, it is suggested to use only substitution operations
	with time-dependent costs inversely proportional to transition frequencies
	whenever the timing of sequences is central. This OM variant, coined
	dynamic Hamming matching, is applied to the question of the scheduling
	of paid work where timing is critical (1985 and 1999 French time
	use surveys, N = 7,908) along with three classical OM variants (Hamming
	and Levenshtein I and II). As expected, the two Hamming dissimilarity
	measures fare better to identify patterns of workday schedules, as
	measured by entropy, than the two Levenshtein ones.},
  doi = {10.1177/0049124110362526},
  owner = {Satu Helske},
  timestamp = {2015.12.16}
}

@ARTICLE{Liu1989,
  author = {Liu, Dong C and Nocedal, Jorge},
  title = {On the Limited Memory BFGS Method for Large Scale Optimization},
  journal = {Mathematical Programming},
  year = {1989},
  volume = {45},
  pages = {503--528},
  number = {1},
  doi = {10.1007/BF01589116},
  owner = {Satu Helske},
  publisher = {Springer},
  timestamp = {2015.09.23}
}

@BOOK{Lopez2008,
  title = {Markov Models for Longitudinal Course of Youth Bipolar Disorder},
  publisher = {ProQuest},
  year = {2008},
  author = {Lopez, Adriana},
  address = {Ann Arbor, MI},
  owner = {Satu Helske},
  timestamp = {2015.10.14},
  url = {http://d-scholarship.pitt.edu/6524/1/LopezAdrianaApril23.pdf}
}

@ARTICLE{Mueller2007,
  author = {M{\"u}ller, Nicolas S{\'e}verin and Studer, Matthias and Ritschard,
	Gilbert},
  title = {Classification de Parcours de Vie {\`a} l'Aide de l'Optimal Matching},
  journal = {XIVe Rencontre de la Soci{\'e}t{\'e} francophone de classification
	(SFC 2007)},
  year = {2007},
  pages = {157--160},
  owner = {Satu Helske},
  timestamp = {2015.09.23}
}

@BOOK{MacDonald1997,
  title = {Hidden Markov and Other Models for Discrete-Valued Time Series},
  publisher = {CRC Press},
  year = {1997},
  author = {MacDonald, Iain L and Zucchini, Walter},
  address = {Boca Raton, FL},
  owner = {Satu Helske},
  timestamp = {2015.04.22}
}

@ARTICLE{McVicar2002,
  author = {McVicar, Duncan and Anyadike-Danes, Michael},
  title = {Predicting Successful and Unsuccessful Transitions from School to
	Work by Using Sequence Methods},
  journal = {Journal of the Royal Statistical Society: Series A (Statistics in
	Society)},
  year = {2002},
  volume = {165},
  pages = {317--334},
  number = {2},
  __markedentry = {[samahels:]},
  doi = {10.1111/1467-985X.00641},
  owner = {samahels},
  publisher = {Wiley Online Library},
  timestamp = {2013.08.28}
}

@MANUAL{Neuwirth2014,
  title = {\pkg{RColorBrewer}: \pkg{ColorBrewer} Palettes},
  author = {Erich Neuwirth},
  year = {2014},
  note = {\proglang{R}~Package Version~1.1-2},
  owner = {Satu Helske},
  timestamp = {2015.10.15},
  url = {http://CRAN.R-project.org/package=RColorBrewer}
}

@ARTICLE{Nocedal1980,
  author = {Nocedal, Jorge},
  title = {Updating Quasi-Newton Matrices with Limited Storage},
  journal = {Mathematics of Computation},
  year = {1980},
  volume = {35},
  pages = {773--782},
  number = {151},
  doi = {10.1090/S0025-5718-1980-0572855-7},
  owner = {Satu Helske},
  timestamp = {2015.09.23}
}

@ARTICLE{OConnell2011,
  author = {Jared O'Connell and S{\o}ren H{\o}jsgaard},
  title = {Hidden Semi Markov Models for Multiple Observation Sequences: The
	\pkg{mhsmm} Package for \proglang{R}},
  journal = {Journal of Statistical Software},
  year = {2011},
  volume = {39},
  pages = {1--22},
  number = {4},
  doi = {10.18637/jss.v039.i04},
  owner = {Satu Helske},
  timestamp = {2015.12.16}
}

@ARTICLE{Pol1990,
  author = {van de Pol, Frank and Langeheine, Rolf},
  title = {Mixed Markov Latent Class Models},
  journal = {Sociological Methodology},
  year = {1990},
  volume = {20},
  pages = {213--247},
  doi = {10.2307/271087},
  owner = {Satu Helske},
  publisher = {JSTOR},
  timestamp = {2015.04.10}
}

@ARTICLE{Rabiner1989,
  author = {Rabiner, Lawrence},
  title = {A Tutorial on Hidden Markov Models and Selected Applications in Speech
	Recognition},
  journal = {Proceedings of the IEEE},
  year = {1989},
  volume = {77},
  pages = {257--286},
  number = {2},
  doi = {10.1109/5.18626},
  owner = {Satu Helske},
  publisher = {IEEE},
  timestamp = {2014.04.14}
}

@ARTICLE{Kan1987I,
  author = {Rinnooy Kan, AHG and Timmer, GT},
  title = {Stochastic Global Optimization Methods Part {I}: Clustering Methods},
  journal = {Mathematical Programming},
  year = {1987},
  volume = {39},
  pages = {27--56},
  number = {1},
  doi = {10.1007/BF02592070},
  owner = {Satu Helske},
  publisher = {Springer},
  timestamp = {2015.08.26}
}

@ARTICLE{Kan1987II,
  author = {Rinnooy Kan, AHG and Timmer, GT},
  title = {Stochastic Global Optimization Methods Part {II}: Multi-Level Methods},
  journal = {Mathematical Programming},
  year = {1987},
  volume = {39},
  pages = {57--78},
  number = {1},
  doi = {10.1007/BF02592071},
  owner = {Satu Helske},
  publisher = {Springer},
  timestamp = {2015.08.26}
}

@MANUAL{Turner2014,
  title = {\pkg{hmm.discnp}: Hidden Markov Models with Discrete Non-Parametric
	Observation Distributions},
  author = {Turner, Rolf and Liu, Limin.},
  year = {2014},
  note = {\proglang{R}~Package Version~0.2-3},
  owner = {Satu Helske},
  timestamp = {2015.04.21},
  url = {http://CRAN.R-project.org/package=hmm.discnp}
}

@INCOLLECTION{Vermunt2008,
  author = {Vermunt, Jeroen K and Tran, Bac and Magidson, Jay},
  title = {Latent Class Models in Longitudinal Research},
  publisher = {Elsevier, Burlington, MA},
  year = {2008},
  editor = {Menard, S},
  series = {Handbook of Longitudinal Research: Design, Measurement, and Analysis},
  pages = {373--385},
  journal = {Handbook of longitudinal research: Design, measurement, and analysis},
  owner = {Satu Helske},
  timestamp = {2014.07.01}
}

@ARTICLE{Visser2010,
  author = {Visser, Ingmar and Speekenbrink, Maarten},
  title = {\pkg{depmixS4}: An \proglang{R}-package for Hidden Markov Models},
  journal = {Journal of Statistical Software},
  year = {2010},
  volume = {36},
  pages = {1--21},
  number = {7},
  doi = {10.18637/jss.v036.i07},
  owner = {Satu Helske},
  timestamp = {2015.04.21}
}

@MANUAL{nloptr,
  title = {\pkg{nloptr}: \proglang{R} Interface to \pkg{NLopt}},
  author = {Ypma, Jelmer and Borchers, Hans W. and Eddelbuettel, Dirk},
  year = {2014},
  note = {\proglang{R}~Package Version~1.0.4},
  owner = {Satu Helske},
  timestamp = {2015.12.16},
  url = {http://CRAN.R-project.org/package=nloptr}
}

@BOOK{Blanchard2014,
  title = {Advances in Sequence Analysis: Theory, Method, Applications},
  publisher = {Springer New York Heidelberg Dordrecht London},
  year = {2014},
  editor = {Blanchard, Philippe and B{\"u}hlmann, Felix and Gauthier, Jacques-Antoine},
  doi = {10.1007/978-3-319-04969-4},
  owner = {Satu Helske},
  timestamp = {2015.05.04}
}

@Manual{Helske2017a,
  title  = {Visualization tools in the \pkg{seqHMM} package},
  author = {Satu Helske},
  year   = {2017},
  url    = {https://cran.r-project.org/web/packages/seqHMM/vignettes/seqHMM_visualization.pdf},
}

@Manual{Helske2017b,
  title  = {Examples and tips for estimating Markovian models with \pkg{seqHMM}},
  author = {Satu Helske},
  year   = {2017},
  url    = {https://cran.r-project.org/web/packages/seqHMM/vignettes/seqHMM_estimation.pdf},
}

@Manual{Helske2017c,
  title  = {The main algorithms used in the \pkg{seqHMM} package},
  author = {Jouni Helske},
  year   = {2017},
  url    = {https://cran.r-project.org/web/packages/seqHMM/vignettes/seqHMM_algorithms.pdf},
}

@Book{Bartolucci2012,
  title     = {Latent {Markov} models for longitudinal data},
  publisher = {CRC Press},
  year      = {2012},
  author    = {Bartolucci, Francesco and Farcomeni, Alessio and Pennoni, Fulvia},
  address   = {Boca Raton, FL},
  owner     = {Satu Helske},
  timestamp = {2016.02.18},
}

@Article{JSS2019,
  title = {Mixture Hidden {M}arkov Models for Sequence Data: The {seqHMM} Package in {R}},
  author = {Satu Helske and Jouni Helske},
  journal = {Journal of Statistical Software},
  year = {2019},
  volume = {88},
  number = {3},
  pages = {1--32},
  doi = {10.18637/jss.v088.i03},
}

@incollection{Helske2016a,doi = {10.1007/978-3-319-95420-2_11},url = {https://doi.org/10.1007%2F978-3-319-95420-2_11},year = 2018,publisher = {Springer International Publishing},pages = {185--200},author = {Satu Helske and Jouni Helske and Mervi Eerola},title = {Combining Sequence Analysis and Hidden Markov Models in the Analysis of Complex Life Sequence Data},booktitle = {Life Course Research and Social Policies}}

@article{seqHMM,
  author    = "Satu Helske and Jouni Helske",
  title     = "Mixture Hidden {M}arkov Models for Sequence Data: The {seqHMM} Package in {R}",
 journal      = "Journal of Statistical Software",
  year         = "2019",
  volume       = "88",
  number       = "3",
  pages        = "1--32",
  doi          = "10.18637/jss.v088.i03"
}

@Manual{Rcore,
  title        = {\proglang{R}: A Language and Environment for Statistical Computing},
  author       = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address      = {Vienna, Austria},
  year         = {2018},
  url          = {https://www.R-project.org/},
}
  
